# Use Ubuntu as the base image
FROM ubuntu:latest

# Install Java 8
RUN apt-get update && \
    apt-get install -y openjdk-8-jre && \
    apt-get clean;
# Set JAVA_HOME environment variable
ENV JAVA_HOME /usr/lib/jvm/java-8-openjdk-amd64

# Install Miniconda
RUN apt-get install -y wget && \
    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /tmp/miniconda.sh && \
    /bin/bash /tmp/miniconda.sh -b -p /opt/conda && \
    rm /tmp/miniconda.sh

# Add Conda to the PATH
ENV PATH="/opt/conda/bin:${PATH}"
RUN conda config --set always_yes true
RUN conda init

# Create a Conda environment and install software
RUN conda install python
RUN conda install -y -c bioconda hmmer mafft gappa && \
    conda clean -ya